1. Perhaps your term hot keying units may be a bit confused. In the case of unique units, you can only build them out of your fortress, and as far as I know, you cannot change this.
2. Chose a hotkey set up that works for you. Many players I know play random civies, and because it is easy to run into conflicts with the hot keys, most just use the default settings (check the options menu to see them). While I have seen Chichiri's excellent article, other than a post here and there, I have seen no other comprehensive write-ups on the issue.
Some tips:
You can use one hot key to create units from all raxes: for example a key may be assigned to all first units (classical) outta raxes, as long as that rax is selected first. For example, assign your "k" key to make hoplites, tox, and hipps. It's easy to remember and limits the keys you have to remember/hit. With this setting, select your archery, and pressing k will train an tox. Selecting a stable and pressing k will create a hipp and so on. Shift k will make five of them.
Unlike hotkeys, grouping units helps too. For example I group longhouses using the ctr-9 key. If I have four raxes grouped, I hit 9, then k, and four ulfs are created simultaneously. It's fast, convenient, and helps to reduce workload. You can also group a raiding party. That way they are easy to control and find.
Your issues are complex since the hotkeys have many nuances that you will discover by trial and error. Be patient as finding a good set up takes time. When I originally set up my keys, I did it over a couple of weeks, playing, tweaking, playing and tweaking. To my chagrin, with TT, some keys went a little haywire but that's for another post.